In a nutshell rep is a different pool for each network site. So say if I was on this network site with a 3k rep and then joined the autos SE site. There is no way to genuinely know I am knowledgeable in that area without proving it. Hence, having to rebuild rep for that particular area. However once you gain 200 rep on a single network you are automatically given a bonus 100 rep for new networks you join. This way you can forgo a lot of the new user restrictions.
You can learn more about reputation and how it works herehere.